Histone deacetylase as a modulator of pdli expression and activity

ABSTRACT

Disclosed herein is a method for modulating Program Death Receptor Ligand 1 (PDL1) in a cancer cell, comprising contacting the cell with a composition comprising a histone deacetylase (HDAC) inhibitor. Also disclosed is a method for treating a tumor in a subject, comprising administering to the subject a therapeutically effective amount of a composition comprising a histone deacetylase (HDAC) inhibitor and a composition comprising a therapeutically effective amount of a Program Death Receptor Ligand 1 (PDL1) inhibitor, a Programmed Death 1 receptor (PD1) inhibitor, or a combination thereof.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit of U.S. Provisional Application No.61/975,858, filed Apr. 6, 2014, and Application Ser. No. 61/977,003,filed Apr. 8, 2014, which are hereby incorporated herein by reference intheir entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government Support under Grant No. CA153246awarded by the National Institutes of Health. The Government has certainrights in the invention.

BACKGROUND

According to the World Health Organization (WHO), the incidence ofmelanoma is increasing faster than any other cancer (Lens, M. B. &Dawes, M. British Journal of Dermatology 150:179-185 (2004)). With theadvent of new therapies like BRAF inhibitors and ipilimumab, the medianoverall survival for metastatic melanoma is 11-14 months, and currentlythere are no other therapies which offer any additional improvement inoverall survival (Hassel, J. C., et al. Br J Cancer (2010); Korn, E. L.,et al. Journal of clinical oncology: official journal of the AmericanSociety of Clinical Oncology 26:527-534 (2008)). There is a high levelof interest in defining environmental, genetic and host factors whichmight be therapeutic targets.

SUMMARY

Histone deacetylases (HDACs), originally described as histone modifiers,have more recently been demonstrated to modify a variety of otherproteins involved in diverse cellular processes unrelated to thechromatin environment. This includes deacetylation of multiplenon-histone targets, such as proteins involved in cell cycle/apoptosisand immune regulation. This expanded role raises the possibility thatthe effects of HDACs and HDAC inhibitors (HDACi) may affectnon-epigenetic regulatory pathways. In contrast to the well-documentedeffects of HDACi in the control of cell cycle and apoptosis, their rolein immunobiology is still not completely understood, and the reportedimmunological outcomes when using HDACi are heterogeneous. Disclosedherein is evidence showing that the pharmacological or geneticabrogation of a single HDAC, HDAC6, modifies the immunogenicity andproliferation of melanoma cells. Additionally, HDAC6 interacts with andmodulates the activity of STAT3 to control downstream target genes.Among these genes, the Program Death Receptor Ligand 1 (PDL1) is highlysusceptible to this regulatory mechanism involving HDAC6 and STAT3. Theexpression of PDL1 has been shown to be induced in almost every type ofcancer, including solid tumors such as melanoma, and it has beenproposed that this could be one of the main mechanisms used by cancercells to acquire resistance to T-cell killing, by activating thenegative regulatory pathway PD-1 in T-cells. Thus, this particularregulatory mechanism could be explored to design more efficient andtailored therapies to improve the cancer immune response.

Disclosed herein is a method for modulating Program Death ReceptorLigand 1 (PDL1) in a cancer cell, comprising contacting the cell with acomposition comprising a histone deacetylase (HDAC) inhibitor. Alsodisclosed is a method for treating a tumor in a subject, comprisingadministering to the subject a therapeutically effective amount of acomposition comprising a histone deacetylase (HDAC) inhibitor and acomposition comprising a therapeutically effective amount of a ProgramDeath Receptor Ligand 1 (PDL1) inhibitor, a Programmed Death 1 receptor(PD1) inhibitor, or a combination thereof. In some cases, thecomposition is administered in an amount effective to treat or preventthe cancer cells from becoming resistant to T-cell killing.

In some embodiments, the HDAC inhibitor is a selective inhibitor ofhistone deacetylase 6 (HDAC6). Selective HDAC6 inhibitors are shownherein to inactivate the STAT3 pathway and down-regulate its targetgenes, including the expression of PDL1. Non-limiting examples of HDAC6inhibitors include ACY-1215, Tubacin, Tubastatin A, ST-3-06, ST-2-92,Nexturastat A, and Nexturastat B.

In some embodiments, the HDAC inhibitor is a pan class I HDAC inhibitor.HDAC inhibitors with potency against class I HDACs are shown herein toupregulate the expression of PDL1 in melanoma cell lines. Therefore, insome embodiments, a pan class I HDAC inhibitor can be used when thetumor comprise low PDL1 expression. Non-limiting examples of class IHDAC inhibitors include Vorinostat, LBH589, ITF2357, PXD-101,Depsipeptide, MS-275, and MGCD0103.

In some embodiments, the PDL1 inhibitor comprises an antibody thatspecifically binds PDL1, such as BMS-936559 (Bristol-Myers Squibb) orMPDL3280A (Roche). In some embodiments, the PD1 inhibitor comprises anantibody that specifically binds PD1, such as lambrolizumab (Merck),nivolumab (Bristol-Myers Squibb), or MEDI4736 (AstraZeneca).

The disclosed composition can be used in combination with other cancertreatments. For example, the disclosed inhibitors of HDAC, PDL1, PD1, orcombinations thereof can be administered alone or in combination with acancer immunotherapy agent. For example, the cancer immunotherapy agentcan be an antibody that specifically binds CLTA-4, such as ipilimumab(Bristol-Myers Squibb).

The details of one or more embodiments of the invention are set forth inthe accompa-nying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF DRAWINGS

FIGS. 1A and 1B show that HDAC6 knock-down decreases STAT3 activation.FIG. 1A is a western blot of melanoma cell lines knocked-down for HDAC6(HDAC6KD). In parallel was evaluated the proliferation of these cellsand compared to their homologous non-target (NT) shRNA controls. FIG. 1Bis a western blot of HDAC6KD and NT melanoma cells stimulated with IL-6(30 ng/mL).

FIG. 2A is a Heat Map of the gene expression profiles obtained bymicroarray. Genes were clustered according to their properties using thesoftware GeneCluster 3.0. The values for gene expression obtained fromtwo clones for each cell line and compared with their respectivecontrols. Shown are the genes with an over two-fold increase or decreasein both clones. FIG. 2B is an ontology distribution of genes affected inHDAC6KD cells. Ontology report generated by “The database forAnnotation, Visualization and Integrated Discovery (DAVID)”.Quantitative real time PCR validation. FIG. 2C contains bar graphsshowing gene expression in RAW264.7 NT and HDAC6KD cells (2×10⁶/well)untreated or stimulated with LPS (1 g/ml) for 2 hrs, then total RNA wasisolated to analyze the expression of genes affected by HDAC6KD. GAPDHwas used as control. The results are expressed as a percent over controlcells and calculated by the Pfaffl equation. Three experiments wereperformed with similar results. Error bars represent standard deviationfrom triplicates.

FIGS. 3A to 3B show HDAC6 knock-down decreases STAT3 activation. FIG. 3Ashows the presence of HDAC6, ac-tubulin, and tubulin in melanoma celllines knocked-down for HDAC6 (HDAC6KD). In parallel was evaluated theproliferation of these cells and compared to their homologous non-target(NT) shRNA controls. FIG. 3B shows the protein expression in HDAC6KD andNT melanoma cells stimulated with IL-6 (30 ng/mL).

FIG. 4A shows expression of STAT3 target genes in HDAC6KD and NT WM164cells stimulated with IL-6 by qRT-PCR. FIG. 4B shows the expression ofSTAT3, PDL1, and GAPDH in STAT3KD and NT melanoma cells by western blot.

FIGS. 5A and 5C show the expression of PDL1 evaluated in HDAC6KD and NTmelanoma cells by qRT-PCR (FIG. 5A) or Flow cytometry (FIG. 5C). FIG. 5Bshows the expression of HDAC6, PDL1, STAT3, pSTAT3, and GAPDH in HDAC6KDand NT melanoma cells by western blot.

FIG. 6A shows either Flag-STAT3 (top) or Flag-HDAC6 expressed in WM164cells and subjected to immunoprecipitation. HDAC6 and STAT3 wereevaluated in the immunoprecipitated fraction. FIG. 6B shows theexpression of HDAC6, MAPK, pMAPK, c-JUN, p c-JUN, and GAPDH evaluated inHDAC6KD and NT melanoma cells by western blot.

FIG. 6C shows non-target and HDAC6KD cells subjected toimmunoprecipitation using an anti-total acetyl-lysine antibody andevaluated for the presence of c-JUN in the immunoprecipitated fraction.

FIG. 7A shows the in vivo growth of HDAC6KD melanoma cells (and controlnon-target and WT melanoma cells) in immune competent C57BL/6 mice. FIG.7B shows in vivo growth of B16 cells in C57BL/6 mice treated withNexturastat. FIG. 7C shows protein levels of STAT3, pSTAT3, PDL1, andGAPDH in tumor samples treated with Nexturastat. Fogure 7D shows proteinexpression in melanoma cells treated with the HDAC6inh Tubastatin A for48 hours.

FIGS. 8A, 8B and 8C show that HDAC inhibitors decrease cellproliferation of melanoma cells. FIG. 8A shows the structure of HDACinhibitors tested. FIG. 8B shows cell viability of melanoma cellsincubated with LBH589, TSA, Tubastatin A, or Nexturastat A at differentconcentrations for 24 hrs. Error bars represent standard deviation fromtriplicates. This figure is representative of two independentexperiments. FIG. 8C shows tubulin, acetyl-tubulin and acetyl-histone3expression in BRAF-mutated melanoma cell lines treated with HDAC6inhibitors.

FIGS. 9A and 9B show HDAC6 profile of melanoma cell lines. FIG. 9A showsHDAC6 expression in human melanocytes, BRAF mutant, and NRAS mutantmelanoma cell lines. FIG. 9B shows HDAC6 expression in 9 primary humanmelanomas.

FIGS. 10A and 10B show characterization of human (FIG. 10A) and B16murine (FIG. 10B) HDAC6KD melanoma cell lines. Cell lines weretransduced with shRNA either coding for HDAC6 or a non-target sequence.Cells were immunoblotted using specific antibodies to HDAC6, tubulin andacetylated tubulin. Two HDAC6KD clones and two NT controls were analyzedand then subjected to MTS assay. Data is representative of threeexperiments with similar results. FIG. 10C shows expression of fulllength and cleaved protein fragments of PARP, BAX, cleaved caspase 8,and cleaved caspase 3 in HDAC6KD and NT melanoma cells.

FIG. 10D shows cell cycle analysis of NT and HDAC6KD human melanoma celllines stained with propidium iodide. Data is representative of threeexperiments with similar results.

FIGS. 11A to 11C show expression of tumor antigens in Melanoma celllines. FIG. 11A shows expression of tumor antigens in different melanomacells incubated with HDAC6i for 48 hours measured by qRT-PCR. FIG. 11Bshows expression of tumor antigens measured in WM164 non-target andHDAC6KD cells. FIG. 11C shows expression of tumor antigens measured bywestern blot.

FIGS. 12A to 1B show increased MHC1 expression after HDAC6 inhibition inmelanoma cell lines. FIG. 12A shows MHC I expression in NT and HDAC6KDmelanoma cell lines. FIG. 12B shows MHC I expression in wild typemelanoma cell lines treated in vitro with Tubastatin A (3 μM) for 48hours.

FIGS. 13A, 13B, and 13C show that HDAC6 modulates tumor growth in vivo.FIG. 13A shows in vivo tumor growth of C57BL/6 mice injectedsubcutaneously with B16 WT cells. Mice were either untreated or treatedwith the HDAC6 inhibitor Nexturastat B or Tubastatin A via dailyintraperitoneal injection. FIG. 13B shows in vivo growth of C57BL6/miceinjected with B16 HDAC6KD or NT melanoma cells. FIG. 13C shows B16growth in HDAC6 KO C57BL/6 mice and WT control.

FIGS. 14A and 14B show differences in growth of melanoma cells afterHDAC6 inhibition in altered immune systems. FIG. 14A shows in vivogrowth of B16 WT melanoma injected into SCID mice was not significantlydifferent despite treatment with HDAC6 inhibitor Nexturastat B. FIG. 14Bshows in vivo growth of B16 HDAC6KD melanoma cells and controlnon-target cells in C57BL/6mice. Mice were treated with antibodies todeplete CD4, CD8, and NK cells. These findings suggest that changes intumor growth after HDAC6 inhibition are in part, due to the immunerecognition of the tumor.

FIGS. 15A and 15B show characterization of HDAC6KD melanoma cells. FIG.15A shows generation of melanoma monoclonal cell lines with or withoutHDAC6 expression. Melanoma cells were transduced with either shRNAcoding for HDAC6 or a non-target sequence. Cells were immunoblottedusing specific antibodies to HDAC6, tubulin and acetylated tubulin. FIG.15B shows phosphorylation of JAK2 and STAT3 measured in different humanmelanoma NT or HDAC6KD cell lines after stimulation with IL-6. Cellswere lysed and immunoblotted using the specific antibodies above.

FIG. 16 shows quantitative RT-PCR of STAT3 target genes. Total RNA wasisolated from melanoma cell lines NT and HDAC6KD before and aftertreatment with IL-6, and the expressions of STAT3 target genes wereanalyzed by quantitative RT-PCR. The results are expressed as a percentover control cells, and data was normalized by GAPDH expression. Thisexperiment was performed three times with similar results. Error barsrepresent standard deviation from triplicates.

FIGS. 17A to 17C show PDL-1 expression in melanoma HDAC6KD. FIG. 17Ashows PD-L1 expression in HDAC6KO cells versus wild type cells measuredby qRT-PC Rafter IL-6 or DMSO. FIG. 17B shows PD-L1 expression inmelanoma NT and HDAC6KD cell lines analyzed by qRT-PCR after IL-6 (30ng/ml), IFN-g (100 ng/ml), or DMSO. FIG. 17C shows PDL1 expression inHDAC6KD cells analyzed by western blot.

FIGS. 18A and 18B show PDL-1 expression in melanoma STAT3KD and HDAC6KD.FIG. 18A shows STAT3, PDL-1 and GAPDH expression in melanoma monoclonalcell lines with or without STAT3 expression. FIG. 18B shows flowcytometric analysis for PDL-1 in HDACKD, STAT3KD, and non-targetmelanoma before and after IFN-γ stimulation.

FIG. 19 shows characterization of melanoma cell lines afterpharmacologic HDAC6 inhibition. Different melanoma cells lines wereincubated with the HDAC6 inhibitor Tubastatin A (12.5 μM) for 24 hours,followed with stimulation by IL-6 (30 ng/ml). Cells were lysed andimmunoblotted for HDAC6, acTUBULIN, STAT3, pSTAT3-Y705, PD-L1, andGAPDH.

FIG. 20 shows melanoma xenograft analysis. Tumors collected from C57BLmice injected either with B16 NT cells or B16 HDAC6KD were immunoblottedfor HDAC6, acTUBULIN, STAT3, pSTAT3-Y705, PD-L1, and GAPDH. DecreasedSTAT3 phosphorylation and PDL-1 expression are maintained in thesetumors.

FIG. 21 shows selectivity of HDAC inhibitors. The murine melanoma cellline B16 was treated with indicated HDACi at indicated doses for 24hours. Cells were lysed and analyzed for acetylated histone 3,acetylated alpha-tubulin and total alpha tubulin protein.

FIG. 22 shows HDAC inhibitors with potency against class I HDACsupregulate PDL1 expression in vitro. B16, WM983A, Sk-Mel21, WM1366,WM35, and WM793 melanoma cells lines were treated with DMSO (“D”), 10 nMLBH589 (“LB”), 500 nM MGCD0103 (“MG), or 500 nM MS275 (“MS”) for 72hours. PDL1 expression was assessed by flow cytometry. Histograms shownare for PDL1 expression or autofluorescence (solid grey) of 10,000 cellsor more.

FIG. 23 shows PDL1 upregulation by HDAC inhibitors is long lasting.Melanoma cell lines were treated with DMSO, 10 nM LBH589 (squares), 1.5μM ACY1215 (triangles), 500 nM MS275 (diamonds), 500 nM CLB66 (circles),or 500 nM MGCD0103 (X). PDL1 expression at indicated time points wasassessed by flow cytometry. Voltages between time point measurements wasstandardized using rainbow beads with standard emissions. Meanfluorescence intensity minus autofluorescencee is graphed for each timepoint. DMSO treatment was plotted as zero hours.

FIG. 24 shows LBH589 upregulates PDL1 expression in vivo. C57BL/6 micewere injected subcutaneously with 100,000 B16 cells. When tumors becamepalpable, treatment with 15 mg/kg LBH589 via IP injection began on aMon, Wed, Fri schedule. After one week of treatment, mice weresacrificed, tumors harvest and analyzed by flow cytometry for PDL1expression.

FIG. 25 shows HDAC inhibitor-induced PDL1 expression is enhanced byIFN-γ exposure. SKMel21 cells were treated for 72 hours with DMSO, 10 nMLBH589, 10 ng/mL IFN-γ, or LBH589 and IFN-γ. PDL1 expression wasassessed by flow cytometry.

FIG. 26 shows knockdowns of individual HDACs does not recapitulate theenhanced PDL1 expression seen in HDAC inhibitor treated melanoma. SingleHDAC knockdowns of class I HDACs were generated as well as a NT controlin the melanoma cell line SKMel21. Cells were assessed by flow cytometryfor PDL1 expression.

FIG. 27 shows combining LBH589 with PDL1 blockade can enhance survival.C57BL/6 mice were injected subcutaneously with 100,000 B16 cells. On day10, they were treated with 15 mg/kg LBH589 three times weekly, anti-PDL1twice weekly, combination of LBH589 and anti-PDL1, or dextrose controlinjections. Treatment continued for three weeks and mice were monitoredfor survival.

DETAILED DESCRIPTION

A major challenge to turning on the immune system to attack cancer isthat the immune system consists of an elaborate network of checks andbalances to avoid over-activation which could harm healthy tissue. Forcancer to develop, tumor cells need to hide from the immune systems. Onemechanism tumor cells use to hide is exploiting the checks and balancesthat are in place for down-regulation, by hijacking so called “immunecheck points” that regulate T-cell activation. Several co-stimulatorypathways have been characterized, including both, activating andinhibiting pathways that determine T-cell activation.

Among several co-stimulatory pathways required for T-cell regulation,the CTLA-4 (cytotoxic T-lymphocyte-associated antigen 4)/B7 inhibitorypathway has been the first target for a pharmaceutical intervention.This pathway is one potential checkpoint that has been hijacked by sometumors to avoid T-cell activation. It predominantly regulates T-cells atthe stage of initial T-cell activation. CTLA-4 is expressed within 48hours after T-cell activation and provides negative signaling thatde-activates the T-cell. Inhibition of CTLA-4 by antibodies such asipilumimab (BMS' Yervoy) or AZN's tremelimumab has resulted in responserate in the 10-15% range in melanoma patients.

Programmed death 1 (PD-1) receptor and PD ligand (PD-L) is anotherinhibitory pathway that down regulates T-cell activation. PD-1activities include the inhibition on T-cells during long-term antigenexposure, as happens in chronic viral infections and cancers. T-celldown-regulation is mediated by the interaction of two cell surfacemolecules (1) PD1 that resides on the T-cell and (2) its ligand PDL1that sits on the tumor cell. To overcome this down-regulation or T-cellblockade, the PD1/PDL1 interactions needs to be blocked. Such a reversalof the down regulation can be achieved using antibodies, either againstthe PD1 receptor that blocks the inhibition of the T-cell side oragainst the ligand PDL1 that blocks the inhibitor on the tumor side.

Histone deacetylases (HDACs) are attractive targets due to theavailability of a broad spectrum of inhibitors targeting their enzymaticactivity (HDACi). HDACs, originally described as histone modifiers, haverecently been demonstrated to modify a variety of other proteinsinvolved in diverse cellular processes unrelated to the chromatinenvironment. This includes deacetylation of multiple non-histonetargets, such as proteins involved in cell cycle/apoptosis and immuneregulation (Woan, K. V., et al. Immunol Cell Biol 90:55-65 (2012);Villagra, A., et al. Oncogene 29:157-173 (2010)). This expanded rolesuggests the possibility that the effects of HDACs and HDACi may includenon-epigenetic regulatory pathways.

Selective HDAC6 inhibitors are shown herein to inactivate the STAT3pathway and down-regulate its target genes, including the expression ofPDL1. However, HDAC inhibitors with potency against class I HDACs areshown herein to upregulate the expression of PDL1 in melanoma celllines. Therefore, in some embodiments, a pan class I HDAC inhibitor canbe used when the tumor comprise low PDL1 expression.

A variety of HDAC6 inhibitors have been investigated (Butler et al.,“Rational Design and Simple Chemistry Yield a Superior, NeuroprotectiveHDAC6 Inhibitor, Tubastatin A,” J Am Chem Soc 2010, 132(31):10842-10846; Kalin et al., “Second-Generation Histone Deacetylase 6Inhibitors Enhance the Immunosuppressive Effects of Foxp3+T-RegulatoryCells,” J Med Chem 2012, 55(2):639-651). Non-limiting examples includeACY-1215, Tubacin, Tubastatin A, ST-3-06, ST-2-92, Nexturastat A, andNexturastat B.

Non-limiting examples of class I HDAC inhibitors include Vorinostat,LBH589, ITF2357, PXD-101, Depsipeptide, MS-275, and MGCD0103.

The disclosed HDAC inhibitors (pan or specific) can be used alone or incombination with a PD1 or PDL1 inhibitor to treat a tumor in a subject.In some embodiments, the PDL1 inhibitor comprises an antibody thatspecifically binds PDL1, such as BMS-936559 (Bristol-Myers Squibb) orMPDL3280A (Roche). In some embodiments, the PD1 inhibitor comprises anantibody that specifically binds PD1, such as lambrolizumab (Merck),nivolumab (Bristol-Myers Squibb), or MEDI4736 (AstraZeneca). Humanmonoclonal antibodies to PD-1 and methods for treating cancer usinganti-PD-1 antibodies alone or in combination with otherimmunotherapeutics are described in U.S. Pat. No. 8,008,449, which isincorporated by reference for these antibodies. Anti-PD-L1 antibodiesand uses therefor are described in U.S. Pat. No. 8,552,154, which isincorporated by reference for these antibodies. Anticancer agentcomprising anti-PD-1 antibody or anti-PD-L1 antibody are described inU.S. Pat. No. 8,617,546, which is incorporated by reference for theseantibodies.

The disclosed compositions and methods can be used in combination withother cancer immunotherapies. There are two distinct types ofimmunotherapy: passive immunotherapy uses components of the immunesystem to direct targeted cytotoxic activity against cancer cells,without necessarily initiating an immune response in the patient, whileactive immunotherapy actively triggers an endogenous immune response.Passive strategies include the use of the monoclonal antibodies (mAbs)produced by B cells in response to a specific antigen. The developmentof hybridoma technology in the 1970s and the identification oftumor-specific antigens permitted the pharmaceutical development of mAbsthat could specifically target tumor cells for destruction by the immunesystem. Thus far, mAbs have been the biggest success story forimmunotherapy; the top three best-selling anticancer drugs in 2012 weremAbs. Among them is rituximab (Rituxan, Genentech), which binds to theCD20 protein that is highly expressed on the surface of B cellmalignancies such as non-Hodgkin's lymphoma (NHL). Rituximab is approvedby the FDA for the treatment of NHL and chronic lymphocytic leukemia(CLL) in combination with chemotherapy. Another important mAb istrastuzumab (Herceptin; Genentech), which revolutionized the treatmentof HER2 (human epidermal growth factor receptor 2)-positive breastcancer by targeting the expression of HER2.

In order to actively drive an antitumor immune response, therapeuticcancer vaccines have been developed. Unlike the prophylactic vaccinesthat are used preventatively to treat infectious diseases, therapeuticvaccines are designed to treat established cancer by stimulating animmune response against a specific tumor-associated antigen. In 2010,sipuleucel-T (Provenge; Dendreon Corporation) was approved by the FDAfor the treatment of metastatic, castration-resistant prostate cancerbased on the results of the IMPACT (Immunotherapy ProstateAdenocarcinoma Treatment) trial in which it improved OS by 4.1 monthsand reduced the risk of death by 22% versus placebo. The advantage ofactive immunotherapies is that they have the potential to providelong-lasting anticancer activity by engaging both the innate andadaptive arms of the immune response. While mAbs are typicallyconsidered passive immunotherapies, there is increasing evidence thatthey also induce an adaptive immune response via a “vaccination-like”effect.

Generating optimal “killer” CD8 T cell responses also requires T cellreceptor activation plus co-stimulation, which can be provided throughligation of tumor necrosis factor receptor family members, includingOX40 (CD134) and 4-1BB (CD137). OX40 is of particular interest astreatment with an activating (agonist) anti-OX40 mAb augments T celldifferentiation and cytolytic function leading to enhanced anti-tumorimmunity against a variety of tumors.

Numerous anti-cancer drugs are available for combination with thepresent method and compositions. The following is a non-exhaustive listsof anti-cancer (anti-neoplastic) drugs that can be used in conjunctionwith irradiation: Acivicin; Aclarubicin; Acodazole Hydrochloride;AcrQnine; Adozelesin; Aldesleukin; Altretamine; Ambomycin; AmetantroneAcetate; Aminoglutethimide; Amsacrine; Anastrozole; Anthramycin;Asparaginase; Asperlin; Azacitidine; Azetepa; Azotomycin; Batimastat;Benzodepa; Bicalutamide; Bisantrene Hydrochloride; Bisnafide Dimesylate;Bizelesin; Bleomycin Sulfate; Brequinar Sodium; Bropirimine; Busulfan;Cactinomycin; Calusterone; Caracemide; Carbetimer; Carboplatin;Carmustine; Carubicin Hydrochloride; Carzelesin; Cedefingol;Chlorambucil; Cirolemycin; Cisplatin; Cladribine; Crisnatol Mesylate;Cyclophosphamide; Cytarabine; Dacarbazine; Dactinomycin; DaunorubicinHydrochloride; Decitabine; Dexormaplatin; Dezaguanine; DezaguanineMesylate; Diaziquone; Docetaxel; Doxorubicin; Doxorubicin Hydrochloride;Droloxifene; Droloxifene Citrate; Dromostanolone Propionate; Duazomycin;Edatrexate; Eflomithine Hydrochloride; Elsamitrucin; Enloplatin;Enpromate; Epipropidine; Epirubicin Hydrochloride; Erbulozole;Esorubicin Hydrochloride; Estramustine; Estramustine Phosphate Sodium;Etanidazole; Ethiodized Oil I 131; Etoposide; Etoposide Phosphate;Etoprine; Fadrozole Hydrochloride; Fazarabine; Fenretinide; Floxuridine;Fludarabine Phosphate; Fluorouracil; Flurocitabine; Fosquidone;Fostriecin Sodium; Gemcitabine; Gemcitabine Hydrochloride; Gold Au 198;Hydroxyurea; Idarubicin Hydrochloride; Ifosfamide; Ilmofosine;Iproplatin; Irinotecan Hydrochloride; Lanreotide Acetate; Letrozole;Leuprolide Acetate; Liarozole Hydrochloride; Lometrexol Sodium;Lomustine; Losoxantrone Hydrochloride; Masoprocol; Maytansine;Mechlorethamine Hydrochloride; Megestrol Acetate; Melengestrol Acetate;Melphalan; Menogaril; Mercaptopurine; Methotrexate; Methotrexate Sodium;Metoprine; Meturedepa; Mitindomide; Mitocarcin; Mitocromin; Mitogillin;Mitomalcin; Mitomycin; Mitosper; Mitotane; Mitoxantrone Hydrochloride;Mycophenolic Acid; Nocodazole; Nogalamycin; Ormaplatin; Oxisuran;Paclitaxel; Pegaspargase; Peliomycin; Pentamustine; Peplomycin Sulfate;Perfosfamide; Pipobroman; Piposulfan; Piroxantrone Hydrochloride;Plicamycin; Plomestane; Porfimer Sodium; Porfiromycin; Prednimustine;Procarbazine Hydrochloride; Puromycin; Puromycin Hydrochloride;Pyrazofurin; Riboprine; Rogletimide; Safmgol; Safingol Hydrochloride;Semustine; Simtrazene; Sparfosate Sodium; Sparsomycin; SpirogermaniumHydrochloride; Spiromustine; Spiroplatin; Streptonigrin; Streptozocin;Strontium Chloride Sr 89; Sulofenur; Talisomycin; Taxane; Taxoid;Tecogalan Sodium; Tegafur; Teloxantrone Hydrochloride; Temoporfin;Teniposide; Teroxirone; Testolactone; Thiamiprine; Thioguanine;Thiotepa; Tiazofurin; Tirapazamine; Topotecan Hydrochloride; ToremifeneCitrate; Trestolone Acetate; Triciribine Phosphate; Trimetrexate;Trimetrexate Glucuronate; Triptorelin; Tubulozole Hydrochloride; UracilMustard; Uredepa; Vapreotide; Verteporfin; Vinblastine Sulfate;Vincristine Sulfate; Vindesine; Vindesine Sulfate; Vinepidine Sulfate;Vinglycinate Sulfate; Vinleurosine Sulfate; Vinorelbine Tartrate;Vinrosidine Sulfate; Vinzolidine Sulfate; Vorozole; Zeniplatin;Zinostatin; Zorubicin Hydrochloride.

The cancer of the disclosed methods can be any cell in a subjectundergoing unregulated growth, invasion, or metastasis. In some aspects,the cancer can be any neoplasm or tumor for which radiotherapy iscurrently used. Alternatively, the cancer can be a neoplasm or tumorthat is not sufficiently sensitive to radiotherapy using standardmethods. Thus, the cancer can be a sarcoma, lymphoma, leukemia,carcinoma, blastoma, or germ cell tumor. A representative butnon-limiting list of cancers that the disclosed compositions can be usedto treat include lymphoma, B cell lymphoma, T cell lymphoma, mycosisfungoides, Hodgkin's Disease, myeloid leukemia, bladder cancer, braincancer, nervous system cancer, head and neck cancer, squamous cellcarcinoma of head and neck, kidney cancer, lung cancers such as smallcell lung cancer and non-small cell lung cancer,neuroblastoma/glioblastoma, ovarian cancer, pancreatic cancer, prostatecancer, skin cancer, liver cancer, melanoma, squamous cell carcinomas ofthe mouth, throat, larynx, and lung, colon cancer, cervical cancer,cervical carcinoma, breast cancer, epithelial cancer, renal cancer,genitourinary cancer, pulmonary cancer, esophageal carcinoma, head andneck carcinoma, large bowel cancer, hematopoietic cancers; testicularcancer; colon and rectal cancers, prostatic cancer, and pancreaticcancer.

Compositions, Formulations and Methods of Administration

In vivo application of the disclosed compounds, and compositionscontaining them, can be accomplished by any suitable method andtechnique presently or prospectively known to those skilled in the art.For example, the disclosed compounds can be formulated in aphysiologically- or pharmaceutically-acceptable form and administered byany suitable route known in the art including, for example, oral, nasal,rectal, topical, and parenteral routes of administration. As usedherein, the term parenteral includes subcutaneous, intradermal,intravenous, intramuscular, intraperitoneal, and intrastemaladministration, such as by injection. Administration of the disclosedcompounds or compositions can be a single administration, or atcontinuous or distinct intervals as can be readily determined by aperson skilled in the art.

The compounds disclosed herein, and compositions comprising them, canalso be administered utilizing liposome technology, slow releasecapsules, implantable pumps, and biodegradable containers. Thesedelivery methods can, advantageously, provide a uniform dosage over anextended period of time. The compounds can also be administered in theirsalt derivative forms or crystalline forms.

The compounds disclosed herein can be formulated according to knownmethods for preparing pharmaceutically acceptable compositions.Formulations are described in detail in a number of sources which arewell known and readily available to those skilled in the art. Forexample, Remington's Pharmaceutical Science by E. W. Martin (1995)describes formulations that can be used in connection with the disclosedmethods. In general, the compounds disclosed herein can be formulatedsuch that an effective amount of the compound is combined with asuitable carrier in order to facilitate effective administration of thecompound. The compositions used can also be in a variety of forms. Theseinclude, for example, solid, semi-solid, and liquid dosage forms, suchas tablets, pills, powders, liquid solutions or suspension,suppositories, injectable and infusible solutions, and sprays. Thepreferred form depends on the intended mode of administration andtherapeutic application. The compositions also preferably includeconventional pharmaceutically-acceptable carriers and diluents which areknown to those skilled in the art. Examples of carriers or diluents foruse with the compounds include ethanol, dimethyl sulfoxide, glycerol,alumina, starch, saline, and equivalent carriers and diluents. Toprovide for the administration of such dosages for the desiredtherapeutic treatment, compositions disclosed herein can advantageouslycomprise between about 0.1% and 99%, and especially, 1 and 15% by weightof the total of one or more of the subject compounds based on the weightof the total composition including carrier or diluent.

Formulations suitable for administration include, for example, aqueoussterile injection solutions, which can contain antioxidants, buffers,bacteriostats, and solutes that render the formulation isotonic with theblood of the intended recipient; and aqueous and nonaqueous sterilesuspensions, which can include suspending agents and thickening agents.The formulations can be presented in unit-dose or multi-dose containers,for example sealed ampoules and vials, and can be stored in a freezedried (lyophilized) condition requiring only the condition of thesterile liquid carrier, for example, water for injections, prior to use.Extemporaneous injection solutions and suspensions can be prepared fromsterile powder, granules, tablets, etc. It should be understood that inaddition to the ingredients particularly mentioned above, thecompositions disclosed herein can include other agents conventional inthe art having regard to the type of formulation in question.

Compounds disclosed herein, and compositions comprising them, can bedelivered to a cell either through direct contact with the cell or via acarrier means. Carrier means for delivering compounds and compositionsto cells are known in the art and include, for example, encapsulatingthe composition in a liposome moiety. Another means for delivery ofcompounds and compositions disclosed herein to a cell comprisesattaching the compounds to a protein or nucleic acid that is targetedfor delivery to the target cell. U.S. Pat. No. 6,960,648 and U.S.Application Publication Nos. 20030032594 and 20020120100 disclose aminoacid sequences that can be coupled to another composition and thatallows the composition to be translocated across biological membranes.U.S. Application Publication No. 20020035243 also describes compositionsfor transporting biological moieties across cell membranes forintracellular delivery. Compounds can also be incorporated intopolymers, examples of which include poly (D-L lactide-co-glycolide)polymer for intracranial tumors; poly[bis(p-carboxyphenoxy)propane:sebacic acid] in a 20:80 molar ratio (as used in GLIADEL);chondroitin; chitin; and chitosan.

For the treatment of oncological disorders, the compounds disclosedherein can be administered to a patient in need of treatment incombination with other antitumor or anticancer substances and/or withradiation and/or photodynamic therapy and/or with surgical treatment toremove a tumor. These other substances or treatments can be given at thesame as or at different times from the compounds disclosed herein. Forexample, the compounds disclosed herein can be used in combination withmitotic inhibitors such as taxol or vinblastine, alkylating agents suchas cyclophosamide or ifosfamide, antimetabolites such as 5-fluorouracilor hydroxyurea, DNA intercalators such as adriamycin or bleomycin,topoisomerase inhibitors such as etoposide or camptothecin,antiangiogenic agents such as angiostatin, antiestrogens such astamoxifen, and/or other anti-cancer drugs or antibodies, such as, forexample, GLEEVEC (Novartis Pharmaceuticals Corporation) and HERCEPTIN(Genentech, Inc.), respectively, or an immunotherapeutic such asipilimumab and bortezomib.

In certain examples, compounds and compositions disclosed herein can belocally administered at one or more anatomical sites, such as sites ofunwanted cell growth (such as a tumor site or benign skin growth, e.g.,injected or topically applied to the tumor or skin growth), optionallyin combination with a pharmaceutically acceptable carrier such as aninert diluent. Compounds and compositions disclosed herein can besystemically administered, such as intravenously or orally, optionallyin combination with a pharmaceutically acceptable carrier such as aninert diluent, or an assimilable edible carrier for oral delivery. Theycan be enclosed in hard or soft shell gelatin capsules, can becompressed into tablets, or can be incorporated directly with the foodof the patient's diet. For oral therapeutic administration, the activecompound can be combined with one or more excipients and used in theform of ingestible tablets, buccal tablets, troches, capsules, elixirs,suspensions, syrups, wafers, aerosol sprays, and the like.

The tablets, troches, pills, capsules, and the like can also contain thefollowing: binders such as gum tragacanth, acacia, corn starch orgelatin; excipients such as dicalcium phosphate; a disintegrating agentsuch as corn starch, potato starch, alginic acid and the like; alubricant such as magnesium stearate; and a sweetening agent such assucrose, fructose, lactose or aspartame or a flavoring agent such aspeppermint, oil of wintergreen, or cherry flavoring can be added. Whenthe unit dosage form is a capsule, it can contain, in addition tomaterials of the above type, a liquid carrier, such as a vegetable oilor a polyethylene glycol. Various other materials can be present ascoatings or to otherwise modify the physical form of the solid unitdosage form. For instance, tablets, pills, or capsules can be coatedwith gelatin, wax, shellac, or sugar and the like. A syrup or elixir cancontain the active compound, sucrose or fructose as a sweetening agent,methyl and propylparabens as preservatives, a dye and flavoring such ascherry or orange flavor. Of course, any material used in preparing anyunit dosage form should be pharmaceutically acceptable and substantiallynon-toxic in the amounts employed. In addition, the active compound canbe incorporated into sustained-release preparations and devices.

Compounds and compositions disclosed herein, including pharmaceuticallyacceptable salts, or hydrates thereof, can be administeredintravenously, intramuscularly, or intraperitoneally by infusion orinjection. Solutions of the active agent or its salts can be prepared inwater, optionally mixed with a nontoxic surfactant. Dispersions can alsobe prepared in glycerol, liquid polyethylene glycols, triacetin, andmixtures thereof and in oils. Under ordinary conditions of storage anduse, these preparations can contain a preservative to prevent the growthof microorganisms.

The pharmaceutical dosage forms suitable for injection or infusion caninclude sterile aqueous solutions or dispersions or sterile powderscomprising the active ingredient, which are adapted for theextemporaneous preparation of sterile injectable or infusible solutionsor dispersions, optionally encapsulated in liposomes. The ultimatedosage form should be sterile, fluid and stable under the conditions ofmanufacture and storage. The liquid carrier or vehicle can be a solventor liquid dispersion medium comprising, for example, water, ethanol, apolyol (for example, glycerol, propylene glycol, liquid polyethyleneglycols, and the like), vegetable oils, nontoxic glyceryl esters, andsuitable mixtures thereof. The proper fluidity can be maintained, forexample, by the formation of liposomes, by the maintenance of therequired particle size in the case of dispersions or by the use ofsurfactants. Optionally, the prevention of the action of microorganismscan be brought about by various other antibacterial and antifungalagents, for example, parabens, chlorobutanol, phenol, sorbic acid,thimerosal, and the like. In many cases, it will be preferable toinclude isotonic agents, for example, sugars, buffers or sodiumchloride. Prolonged absorption of the injectable compositions can bebrought about by the inclusion of agents that delay absorption, forexample, aluminum monostearate and gelatin.

Sterile injectable solutions are prepared by incorporating a compoundand/or agent disclosed herein in the required amount in the appropriatesolvent with various other ingredients enumerated above, as required,followed by filter sterilization. In the case of sterile powders for thepreparation of sterile injectable solutions, the preferred methods ofpreparation are vacuum drying and the freeze drying techniques, whichyield a powder of the active ingredient plus any additional desiredingredient present in the previously sterile-filtered solutions.

For topical administration, compounds and agents disclosed herein can beapplied in as a liquid or solid. However, it will generally be desirableto administer them topically to the skin as compositions, in combinationwith a dermatologically acceptable carrier, which can be a solid or aliquid. Compounds and agents and compositions disclosed herein can beapplied topically to a subject's skin to reduce the size (and caninclude complete removal) of malignant or benign growths, or to treat aninfection site. Compounds and agents disclosed herein can be applieddirectly to the growth or infection site. Preferably, the compounds andagents are applied to the growth or infection site in a formulation suchas an ointment, cream, lotion, solution, tincture, or the like.

Useful solid carriers include finely divided solids such as talc, clay,microcrystalline cellulose, silica, alumina and the like. Useful liquidcarriers include water, alcohols or glycols or water-alcohol/glycolblends, in which the compounds can be dissolved or dispersed ateffective levels, optionally with the aid of non-toxic surfactants.Adjuvants such as fragrances and additional antimicrobial agents can beadded to optimize the properties for a given use. The resultant liquidcompositions can be applied from absorbent pads, used to impregnatebandages and other dressings, or sprayed onto the affected area usingpump-type or aerosol sprayers, for example.

Thickeners such as synthetic polymers, fatty acids, fatty acid salts andesters, fatty alcohols, modified celluloses or modified mineralmaterials can also be employed with liquid carriers to form spreadablepastes, gels, ointments, soaps, and the like, for application directlyto the skin of the user.

Useful dosages of the compounds and agents and pharmaceuticalcompositions disclosed herein can be determined by comparing their invitro activity, and in vivo activity in animal models. Methods for theextrapolation of effective dosages in mice, and other animals, to humansare known to the art.

Also disclosed are pharmaceutical compositions that comprise a compounddisclosed herein in combination with a pharmaceutically acceptablecarrier. Pharmaceutical compositions adapted for oral, topical orparenteral administration, comprising an amount of a compound constitutea preferred aspect. The dose administered to a patient, particularly ahuman, should be sufficient to achieve a therapeutic response in thepatient over a reasonable time frame, without lethal toxicity, andpreferably causing no more than an acceptable level of side effects ormorbidity. One skilled in the art will recognize that dosage will dependupon a variety of factors including the condition (health) of thesubject, the body weight of the subject, kind of concurrent treatment,if any, frequency of treatment, therapeutic ratio, as well as theseverity and stage of the pathological condition.

Definitions

The term “subject” refers to any individual who is the target ofadministration or treatment. The subject can be a vertebrate, forexample, a mammal. Thus, the subject can be a human or veterinarypatient. The term “patient” refers to a subject under the treatment of aclinician, e.g., physician.

The term “therapeutically effective” refers to the amount of thecomposition used is of sufficient quantity to ameliorate one or morecauses or symptoms of a disease or disorder. Such amelioration onlyrequires a reduction or alteration, not necessarily elimination.

The term “treatment” refers to the medical management of a patient withthe intent to cure, ameliorate, stabilize, or prevent a disease,pathological condition, or disorder. This term includes activetreatment, that is, treatment directed specifically toward theimprovement of a disease, pathological condition, or disorder, and alsoincludes causal treatment, that is, treatment directed toward removal ofthe cause of the associated disease, pathological condition, ordisorder. In addition, this term includes palliative treatment, that is,treatment designed for the relief of symptoms rather than the curing ofthe disease, pathological condition, or disorder; preventativetreatment, that is, treatment directed to minimizing or partially orcompletely inhibiting the development of the associated disease,pathological condition, or disorder; and supportive treatment, that is,treatment employed to supplement another specific therapy directedtoward the improvement of the associated disease, pathologicalcondition, or disorder.

The term “prevent” refers to a treatment that forestalls or slows theonset of a disease or condition or reduced the severity of the diseaseor condition. Thus, if a treatment can treat a disease in a subjecthaving symptoms of the disease, it can also prevent that disease in asubject who has yet to suffer some or all of the symptoms.

The term “inhibit” refers to a decrease in an activity, response,condition, disease, or other biological parameter. This can include butis not limited to the complete ablation of the activity, response,condition, or disease. This may also include, for example, a 10%reduction in the activity, response, condition, or disease as comparedto the native or control level. Thus, the reduction can be a 10, 20, 30,40, 50, 60, 70, 80, 90, 100%, or any amount of reduction in between ascompared to native or control levels.

The term “antibody” refers to natural or synthetic antibodies thatselectively bind a target antigen. The term includes polyclonal andmonoclonal antibodies. In addition to intact immunoglobulin molecules,also included in the term “antibodies” are fragments or polymers ofthose immunoglobulin molecules, and human or humanized versions ofimmunoglobulin molecules that selectively bind the target antigen.

Antibodies that can be used in the disclosed compositions and methodsinclude whole immunoglobulin (i.e., an intact antibody) of any class,fragments thereof, and synthetic proteins containing at least theantigen binding variable domain of an antibody. The variable domainsdiffer in sequence among antibodies and are used in the binding andspecificity of each particular antibody for its particular antigen.However, the variability is not usually evenly distributed through thevariable domains of antibodies. It is typically concentrated in threesegments called complementarity determining regions (CDRs) orhypervariable regions both in the light chain and the heavy chainvariable domains. The more highly conserved portions of the variabledomains are called the framework (FR). The variable domains of nativeheavy and light chains each comprise four FR regions, largely adopting abeta-sheet configuration, connected by three CDRs, which form loopsconnecting, and in some cases forming part of, the beta-sheet structure.The CDRs in each chain are held together in close proximity by the FRregions and, with the CDRs from the other chain, contribute to theformation of the antigen binding site of antibodies.

Also disclosed are fragments of antibodies which have bioactivity. Thefragments, whether attached to other sequences or not, includeinsertions, deletions, substitutions, or other selected modifications ofparticular regions or specific amino acids residues, provided theactivity of the fragment is not significantly altered or impairedcompared to the nonmodified antibody or antibody fragment.

Techniques can also be adapted for the production of single-chainantibodies specific to an antigenic protein of the present disclosure.Methods for the production of single-chain antibodies are well known tothose of skill in the art. A single chain antibody can be created byfusing together the variable domains of the heavy and light chains usinga short peptide linker, thereby reconstituting an antigen binding siteon a single molecule. Single-chain antibody variable fragments (scFvs)in which the C-terminus of one variable domain is tethered to theN-terminus of the other variable domain via a 15 to 25 amino acidpeptide or linker have been developed without significantly disruptingantigen binding or specificity of the binding. The linker is chosen topermit the heavy chain and light chain to bind together in their properconformational orientation.

Divalent single-chain variable fragments (di-scFvs) can be engineered bylinking two scFvs. This can be done by producing a single peptide chainwith two VH and two VL regions, yielding tandem scFvs. ScFvs can also bedesigned with linker peptides that are too short for the two variableregions to fold together (about five amino acids), forcing scFvs todimerize. This type is known as diabodies. Diabodies have been shown tohave dissociation constants up to 40-fold lower than correspondingscFvs, meaning that they have a much higher affinity to their target.Still shorter linkers (one or two amino acids) lead to the formation oftrimers (triabodies or tribodies). Tetrabodies have also been produced.They exhibit an even higher affinity to their targets than diabodies.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a substantially homogeneous population of antibodies,i.e., the individual antibodies within the population are identicalexcept for possible naturally occurring mutations that may be present ina small subset of the antibody molecules. The monoclonal antibodiesherein specifically include “chimeric” antibodies in which a portion ofthe heavy and/or light chain is identical with or homologous tocorresponding sequences in antibodies derived from a particular speciesor belonging to a particular antibody class or subclass, while theremainder of the chain(s) is identical with or homologous tocorresponding sequences in antibodies derived from another species orbelonging to another antibody class or subclass, as well as fragments ofsuch antibodies, as long as they exhibit the desired antagonisticactivity.

The term “specifically binds”, as used herein, when referring to apolypeptide (including antibodies) or receptor, refers to a bindingreaction which is determinative of the presence of the protein orpolypeptide or receptor in a heterogeneous population of proteins andother biologics. Thus, under designated conditions (e.g. immunoassayconditions in the case of an antibody), a specified ligand or antibody“specifically binds” to its particular “target” (e.g. an antibodyspecifically binds to an endothelial antigen) when it does not bind in asignificant amount to other proteins present in the sample or to otherproteins to which the ligand or antibody may come in contact in anorganism. Generally, a first molecule that “specifically binds” a secondmolecule has an affinity constant (Ka) greater than about 10⁵ M⁻¹ (e.g.,10⁶ M⁻¹, 10⁷ M⁻¹, 10⁸ M⁻¹, 10⁹ M⁻¹, 10¹⁰ M⁻¹, 10¹¹ M⁻¹, and 10¹² M⁻¹ ormore) with that second molecule.

The term “cancer” or “malignant neoplasm” refers to a cell that displaysuncontrolled growth, invasion upon adjacent tissues, and oftenmetastasis to other locations of the body.

A number of embodiments of the invention have been described.Nevertheless, it will be understood that various modifications may bemade without departing from the spirit and scope of the invention.Accordingly, other embodiments are within the scope of the followingclaims.

EXAMPLES Example 1: HDAC6 as a Modulator of PDL1 Expression and Activity

Results

HDAC6 is a 131KDa protein considered to be a key regulator ofcytoskeleton dynamics and cell-cell interactions (Hubbert, C., et al.Nature 417:455-458 (2002); Valenzuela-Fernández, A., et al. Trends inCell Biology 18:291-297 (2008)). Although this HDAC is predominantlycytoplasmic, studies have demonstrated its presence in nuclear extractsand its recruitment to gene promoter regions (Toropainen, S., et al. JMol Biol. 400:284-294 (2010)). HDAC6 has been reported to beover-expressed in several cancer types, including ovarian cancer,prostate cancer and acute myeloid leukemia (AML) (Aldana-Masangkay, G.I., et al. J Biomed Biotechnol 2011:875824 (2010)). As shown in FIG. 1,HDAC6 is also over-expressed in several melanoma tumors. Recently, HDAC6has been implicated in other cellular processes, including themodulation of immune responses (Serrador, J. M., et al. Immunity20:417-428 (2004); Kalin, J. H., et al. J Med Chem. (2012)). This isconsistent with microarray data analyzing the gene expression profile(GEP) of untreated and LPS-treated RAW264.7 macrophages in which HDAC6was knocked down using specific shRNA (HDAC6KD) or treated with controlshRNA non-coding for any mouse mRNA (non-target, NT). 1542 genes weredown-regulated and 775 were up-regulated in HDAC6KD cells (FIG. 2A).Their ontology distribution revealed important changes in bothimmune-related and apoptosis/cell cycle control genes (FIG. 2B). Aninteresting finding gathered from the GEP analysis was thedown-regulation of almost every STAT3 target gene in HDAC6KD cells,suggesting the potential participation of STAT3 in the outcome that isobserved in the absence of HDAC6 (FIG. 2C). Similarly, severalpreviously described c-Jun target genes were down-regulated, suggestingthat the inhibition of HDAC6 affected the MAPK pathway as well.

STAT3 activation can be achieved by different stimuli and is often thepoint of convergence for many signaling pathways triggered by cytokines,growth factors and other stimuli, being considered by itself anoncogene. Hyperactivation and/or constitutive activation of STAT3 hasbeen found in a wide range of tumors and transformed cell lines. Inparticular, constitutively active STAT3 has been reported in more than70% of solid and hematological tumors, including melanoma and lungcancer (Kortylewski, M., et al. Cancer Metastasis Rev 24:315-327 (2005);Yu, H., et al. Nat Rev Immunol. 7:41-51 (2007)). There are numerousreports describing the effect of STAT3 manipulation upon tumor growth,survival, invasiveness, metastatic potential, angiogenesis, andimmune-escape. In fact, the over-expression of constitutive active STAT3(STAT3c) leads to the immortalization of non-malignant cell lines(Regis, G., et al. Seminars in Cell &amp; Developmental Biology19:351-359 (2008)). Hyperactivity of STAT3 also deregulates theexpression of several important cytokines such as IL-6 and IL-10.Interestingly, HDAC6 interacts with STAT3 and is recruited to andregulates the expression of IL10 and IL6 genes.

Given these findings, as well as the well known role of STAT3deregulation in the pathogenesis of melanoma, a study was conducted todetermine whether the absence of HDAC6 affected the activation of theJAK/STAT3 pathway in melanoma cells. By using lentiviral HDAC6 shRNA,stable HDAC6KD cell lines were generated in several melanoma cell linescarrying either NRAS (SKMEL21, SKMEL103, IPC298) or BRAF (WM164, WM35,WM983, WM795) mutations. Of note, all HDAC6KD cell lines demonstratedslower proliferation rates when compared with their respectivenon-target shRNA control stable cell lines (FIG. 3A, representative fromall cell lines analyzed). When the activation of the Jak2/STAT3 pathwaywas analyzed in these HDAC6KD cells, there was diminishedphosphorylation of the Ser-727 and Tyr-705 residues of STAT3 upon IL-6stimulation (similar results obtained upon IL-10 and IFNγ stimulation)(FIG. 3B, lines 4 and 5). Recent reports have assigned the key role ofacetylation over the activation of STAT3, a process mediated mainly byCBP/p300 acetylation and class I HDAC deacetylation (Togi, S., et al.Biochem Biophys Res Commun. 379:616-620 (2009); Lee, H., et al. ProcNatl Acad Sci USA 109:7765-7769 (2012). Taking this antecedent intoconsideration, the acetylation status of STAT3 was analyzed. However,major differences in its acetylation status in the absence of HDAC6(FIG. 1B, line 6) was did not detected, suggesting that the effect ofHDAC6 on its activation does not depend on a direct deacetylation ofSTAT3.

STAT3 must be phosphorylated in order to be translocated to the nucleusand properly exert its function over target genes (Ihle, J. N. Currentopinion in cell biology 13:211-217 (2001)). Therefore, the diminishedphosphorylation of STAT3 observed in the absence of HDAC6 mightinterfere with the activation of STAT3 target genes. To answer thisquestion well defined STAT3 target genes were selected and theirexpression measured upon IL-6 stimulation. An important reduction in themRNA was observed for all tested genes, including CDKN1A, SOCS1, SOCS3,IL10, FOS and MYC (FIG. 4A).

The GEP microarray data in HDAC6KD macrophages revealed changes inimmune related genes. Among these genes, an 8-fold decrease in theexpression of PDL1 (CD274) was observed. This finding was validated byqRT-PCR in primary macrophages isolated from wild type and HDAC6KO micestimulated with IL-6. PDL1 and PD-L2 are ligands for PD-1, aco-stimulatory molecule that plays an inhibitory role in regulatingT-cell activation. Specifically, the interaction between PDL1 (fromcancer cells) and the PD-1 present on T-cells inhibits T-cellactivation, proliferation, and promotes T-cell apoptosis. The importanceof the interaction of PDL1 and PD-1 has been extensively described in invitro and in vivo models, as well as in clinical studies (Topalian, S.L., et al. Curr Opin Immunol 24:207-212 (2012)), with promisingantitumor results in several preclinical and clinical studies involvingPDL1 blocking antibodies (Pardoll, D. M. Nat Rev Cancer 12:252-264(2012)). Furthermore, PDL1 expression is correlated with poor clinicalprognosis for a number of cancers including renal, breast, andesophageal cancers. As a result, increased PDL1 expression by cancercells remains a fundamental escape mechanism from host immunity, and theunderstanding of molecular mechanisms modulating PDL1 expression couldlead to improved treatments for cancer patients. The expression of PDL1is controlled by several pathways, including those activated by IL-6,IL-10, GM-CSF, TLRs, interferons and TNFα (Francisco, L. M., et al.Immunol Rev 236:219-242 (2010)). In addition, recent reports havedescribed STAT3 as one of the main regulators of PDL1 expression(Wolfle, S. J., et al. Eur J Immunol 41:413-424 (2011)). This findingwas also verified in by evaluating the expression of PDL1 in human andmouse melanoma cells lacking STAT3 (STAT3KD) (FIG. 4B). Therefore, HDAC6could be an indirect regulator of the expression of PDL1 in melanoma viaSTAT3 modulation. Taking this observation into consideration, theexpression of PDL1 in HDAC6KD human melanoma cells stimulated with IL-6was evaluated by qRT-PCR (FIG. 5A). When compared to non-targetcontrols, decreased expression of PDL1 was observed. This result wasalso validated by measuring the PDL1 protein by western blot (FIG. 5B)and flow cytometry (FIG. 5C).

HDAC6 is recruited to regulatory sequences in gene promoters such as MYC(Toropainen, S., et al. J Mol Biol. 400:284-294 (2010)), glucocorticoidreceptor (Govindan, M. V. J Biol Chem. 285:4489-4510 (2010)) andestrogen receptor a-inducible genes (Palijan, A., et al. J Biol Chem.284:30264-30274 (2009)). However, there is no evidence showing thatHDAC6 is directly affecting the acetylation status of chromatin. Infact, the deacetylation of histones by HDAC6 has only been demonstratedby in vitro assays (Todd, P. K., et al. PLoS Genet 6:e1001240 (2010)).Thus, the transcriptional regulatory effects observed for HDAC6 could bemediated by other regulatory factors recruited along with thisdeacetylase to specific DNA sequences. This hypothesis suggests thatHDAC6 may be a regulator of the activation status of these transcriptionfactors, perhaps by modulating their acetylation and/or phosphorylation.HDAC6 and STAT3 are recruited to the same region of the IL-10 promoter,and the recruitment of HDAC6 is impaired when cells are treated with theSTAT3 inhibitor CPA-7. Moreover, the recruitment of STAT3 to the IL-10promoter diminishes considerably in HDAC6KD cells, suggesting that thedown-regulation of PDL1 expression might be a consequence of the effectof HDAC6 on STAT3 activation.

Another potential regulator of the transcriptional regulation of PDL1 isc-Jun. The inhibition of the MEK cascade and the subsequent c-Juninactivation may lead to the down-regulation of PDL1. This phenomena isalso observed in BRAF inhibitor-resistant melanoma cells (Jiang, X., etal. Clin Cancer Res 19:598-609 (2013)). HDAC6 interacts with STAT3 andc-Jun to form stable protein complexes, as detected byco-immunoprecipitation (FIG. 6A). Additionally, HDAC6 does not interferewith the phosphorylation of Erk or c-Jun in melanoma cells (FIG. 6B),suggesting that its effect over the activation of c-Jun target genescould involve another molecular mechanism. In this regard, it has beenproposed that the acetylation of c-Jun modulates its transcriptionalactivity over target genes. Specifically, the acetylation of Lys271 ofc-Jun facilitates its interaction with co-repressors and the subsequentrepression of its target genes (Vries, R. G., et al. EMBO J 20:6095-6103(2001)). To further explore this possibility, the acetylation status ofc-Jun in the absence of HDAC6 was evaluated, demonstrating an importantincrease in its acetylation, suggesting the participation of HDAC6 inthis process (FIG. 6C).

Besides STAT3 and c-Jun, there are no known transcriptional regulatorsor chromatin modifiers affecting the PDL1 promoter. Therefore, it ishighly desirable to perform a more comprehensive analysis of thetranscriptional regulation of this gene. Further understanding of thePDL1 promoter could identify targets to control its expression, which inturn could be used as a therapeutic option to ameliorate cancer immuneevasion mediated by PDL1.

Highly selective HDAC6 inhibitors (HDAC6inh) are currently available,which make this deacetylase a very attractive target to pursue as atherapeutic option. In this context, selective HDAC6 inhibitors, aloneor in combination with other agents, are currently under evaluation inclinical trials, including the ongoing Phase 2 Multiple Myeloma clinicaltrial using the HDAC6inh ACY1215, which has shown important anti-tumoractivity in preliminary studies (Santo, L., et al. Blood 119:2579-2589(2012)). Pan-HDAC inhibitors (pan-HDACi) slows the proliferation andimproves the immunogenicity of melanoma cells (Woods, D. M., et al.Melanoma Res (2013)). However, the non-selective nature of pan-HDACimakes the assumption of the specific participation of HDACs on theseprocesses impossible. As shown in FIG. 2A, HDAC6KD melanoma cells have aslower rate of proliferation when compared to their respective controls.This result was mirrored in melanoma cell lines treated with selectiveHDAC6 inhibitors. The next step was identifying if HDAC6KD would affectthe growth of melanoma cells in vivo. Thus, a delayed tumor growth ofHDAC6KD B16 murine melanoma cells was observed when compared to wildtype or non-target controls (FIG. 7A). A similar result was obtained inanother experiment injecting wild type B16 melanoma cells into C57BL/6mice treated daily with 20 mg/kg of the HDAC6inh Nexturastat A orNexturastat B (FIG. 7B). The amount of PDL1 and activation of STAT3 wasdecreased in tumors isolated after the in vivo treatment with HDAC6inh(FIG. 7C). This observation was also made in melanoma cell lines treatedwith HDAC6inh (FIG. 7D), suggesting the potential role of HDAC6 in thisprocess, and evidence that its deacetylase activity is necessary tomediate this effect.

This delay in tumor growth in HDAC6KD melanoma cells and melanoma cellstreated with HDAC6inh could be a reflection of their diminishedproliferation (as evidenced in in vitro studies) and/or an increase intheir immunogenicity leading to improved immune recognition andclearance.

Conclusions

The expression of PDL1 has been shown to be induced in almost every typeof cancer, including solid tumors such as melanoma, and it has beenproposed that this could be one of the main mechanisms used by cancercells to acquire resistance to T-cell killing, by activating thenegative regulatory pathway PD-1 in T-cells. This is particularlyimportant in the resistance to BRAF inhibitors, phenomena frequentlyassociated with an up-regulation of the expression of PDL1 (Jiang, X.,et al. Clin Cancer Res 19:598-609 (2013)). Therefore, the inhibition ofPDL1 expression could offer new therapeutic options to prevent or revertthe resistance to current therapies aiming to improve the immunerecognition of cancer cells (i.e. PDL1, PD-1, and CTLA-4 blockingantibodies).

Example 2: Histone Deacetylase 6 (HDAC6) as a New Target Modulating theProliferation and Immune-Related Pathways in Melanoma

Histone deacetylases (HDACs), originally described as histone modifiers,have more recently been demonstrated to modify a variety of otherproteins involved in diverse cellular processes unrelated to thechromatin environment. This includes the deacetylation of multiplenon-histone targets, such as proteins involved in cell cycle/apoptosisand immune regulation. Specifically, HDACs have garnered significantinterest due to the availability of drugs that selectively inhibitsHDACs. The pharmacological or genetic abrogation of a single HDAC,HDAC6, modifies the immunogenicity and proliferation of melanoma in bothin vitro and in vivo models.

Using specific HDAC6 inhibitors (HDAC6i), decreased proliferation and G1cell cycle arrest was observed in all melanoma cell lines measured byMTS assay and flow cytometry (FIG. 8). These results were also observedin stable HDAC6 knockdown melanoma cell lines (HDAC6KD) generated byspecific lentiviral shRNA for HDAC6 (FIG. 10D). In addition to theeffects observed in proliferation and apoptosis after inhibiting HDAC6,also shown are important changes in the expression of immune-relatedpathways, including increased expression of MHC (FIG. 12),co-stimulatory molecules, and specific melanoma tumor associatedantigens such as gp100, MART-1, Tyrp1 and Tyrp2 (FIG. 11A-11C).

These in vitro results were further supported by in vivo tumor growthstudies. Delayed tumor growth of inoculated B16 melanoma cells wasobserved in C57BL/6 mice treated with selective HDAC6i (FIG. 13). Asimilar outcome was identified after inoculation of HDAC6KD B16 melanomacells in C57BL/6 mice (FIG. 14A). Such an effect was reverted partiallyin CD4+ and CD8+ depleted C57BL/6 mice challenged with HDAC6KD cells(FIG. 14B), suggesting that the disruption of HDAC6 enhances immunesystem recognition of melanoma cells. This delay in tumor growth couldbe a reflection of their diminished proliferation and an increase intheir immunogenicity leading to improved immune recognition andclearance. These studies provide critical insights into the molecularpathways that are involved in the regulatory role of HDAC6 in cellproliferation, survival, and cytokine signaling of human melanoma cells.Collectively, these data have identified HDAC6 as an attractivetherapeutic target in melanoma.

Example 3: Histone Deacetylase 6 (HDAC6) as a Regulator of PDL-1Expression Through STAT3 Modulation in Melanoma

In spite of the progress made in the understanding of the cell biology,genetics and immunology of melanoma, the outcome for patients withadvanced-stage disease has remained poor with a median survival rangingfrom 2-16 months. Some optimism was recently provided in metastaticmelanoma by the improved clinical outcomes observed in patientsreceiving PDL-1 blocking antibodies.

A better understanding of the environmental, genetic and epigeneticfactors limiting the efficacy of melanoma immunotherapy will provideappropriate partner(s) for combination with Ipilimumab or PD1/PDL1antibodies. Among the epigenetic factors, one member of the histonedeacetylase family, HDAC6, is shown to play a critical role not only inthe regulation of survival/apoptosis of melanoma cells but also inlimiting their immunogenicity and recognition by immune effector cells.In particular, disclosed is a major role of HDAC6 as a modulator of theimmunosuppresive STAT3/IL-6 pathway, resulting in the down-regulation oftolerogenic PDL1 molecules in melanoma cells. By analyzing HDAC6knock-down melanoma cell lines (HDAC6KD), shown herein is theinactivation of the STAT3 pathway and the subsequent down-regulation ofits target genes, including the expression of PDL1. It was also observedthat the PDL1 expression and phosphorylation of STAT3 was decreased inmelanoma isolated from xenograph tumor growth models after in vivotreatment with specific HDAC6 inhibitors.

FIG. 15 shows the characterization of HDAC6KD melanoma cells. FIG. 15Ashows the generation of melanoma monoclonal cell lines with or withoutHDAC6 expression. Melanoma cells were transduced with either shRNAcoding for HDAC6 or a non-target sequence. Cells were immunoblottedusing specific antibodies to HDAC6, tubulin and acetylated tubulin. FIG.15B shows posphorylation of JAK2 and STAT3 measured in different humanmelanoma NT or HDAC6KD cell lines after stimulation with IL-6. Cellswere lysed and immunoblotted using the specific antibodies above.

FIG. 16 shows quantitative RT-PCR of STAT3 target genes. Total RNA wasisolated from melanoma cell lines NT and HDAC6KD before and aftertreatment with IL-6, and the expressions of STAT3 target genes wereanalyzed by quantitative RT-PCR. The results are expressed as a percentover control cells, and data was normalized by GAPDH expression. Thisexperiment was performed three times with similar results. Error barsrepresent standard deviation from triplicates.

FIG. 17 shows PDL-1 expression in melanoma HDAC6KD: FIG. 17A shows totalRNA was isolated from C57BL/mice cells in the HDAC6KO cells versus wildtype cells and was measured by qRT-PCR. FIG. 17B shows total RNAisolated from melanoma cell lines NT and HDAC6KD. The expression of PDL1was analyzed by qRT-PCR after IL-6 (30 ng/ml), IFN-g (100 ng/ml), andDMSO. FIG. 18C shows a Western blot demonstrating decreased PDL1 inHDAC6KD cells.

FIG. 18 shows PDL-1 expression in melanoma STAT3KD and HDAC6KD. FIG. 18Ashows generation of melanoma monoclonal cell lines with or without STAT3expression. Cells were immunoblotted using specific antibodies forSTAT3, PDL-1 and GAPDH. FIG. 18B shows Flow cytometric analysis forPDL-1 in HDACKD, STAT3KD and non target melanoma demonstrates decreasedPDL-1 in HDAC6KD and STAT3KD compared to NT after IFN-g stimulation.

FIG. 19 shows characterization of melanoma cell lines afterpharmacologic HDAC6 inhibition. Different melanoma cells lines wereincubated with the HDAC6 inhibitorTubastatin A (12.5 μM) for 24 hours,followed with stimulation by IL-6 (30 ng/ml). Cells were lysed andimmunoblotted using the specific antibodies listed in the figure.

FIG. 20 shows Melanoma xenograft analysis. Tumors collected from C57BLmice injected either with B16 NT cells or B16 HDAC6KD were lyzed forimmunoblotting analysis using the specific antibodies listed in thefigure. Decreased STAT3 phosphorylation and PDL-1 expression aremaintained in these tumors.

Example 4: Inhibition of Class I Histone Deacetylases Promotes Robustand Durable Enhancement of PDL1 Expression in Melanoma: Rationale forCombination Therapy

Histone deacetylase inhibitors (HDACi) have shown remarkable anti-tumoractivity, leading to FDA approval of two HDACi for the treatment of CTCLand several others currently at various stages of clinical developmentfor the treatment of both solid and hematological malignancies.Treatment with HDACi results in increased expression of pro-inflammatorypromoting surface markers on melanoma cells, promoting enhanced T-cellactivation. Recent clinical trial data has shown that blockade of thePD1/PDL1 interaction is effective in the treatment of melanoma, renalcell and non-small cell lung cancer. Importantly, responses to PD1blocking antibodies were preferentially seen in patients with tumorsexpressing PDL1.

In this Example, HDACi targeting class I HDACs, but not class II, isshown to augment expression of PDL1 in melanoma cells. Two murine andfive human melanoma cell lines were treated for up to 72 hours withDMSO, LBH589 (pan-HDACi), MS275 (class I inhibitor), MGCD0103 (class Iinhibitor), an HDAC6 specific inhibitor, or a class IIa inhibitor (FIG.21). Using flow cytometry, dose dependent, increases in PDL1 expressionwere found in the LBH589, MS275 and MGCD0103 treated groups, but not inthose receiving HDAC6i or class IIa inhibitor, relative to DMSO (FIG.22). Increased expression was noted as early as 24 hours after treatmentand peaked at 72 to 96 hours post-treatment (FIG. 23).

As IFN-γ is known to upregulate the expression of PDL1 in both normaland transformed cells, experiments were conducted to determine whetherthese results were associated with induction of IFN-γ expression by themelanoma cells. However, no detectable levels of IFN-γ were seen ineither nontreated, class I HDACi, or class II HDACi-treated cells.Melanoma cells treated with HDACi in addition to IFN-γ have enhancedexpression of PDL1 relative to either treatment alone (FIG. 25). Tofurther gain insight into the specific HDAC regulating the expression ofPDL1, experiments utilizing knockdowns (KD) of individual class I HDACswere performed. In all KD melanoma cells no increase in PDL1 expressionwas seen (FIG. 26), suggesting that the increased expression of PDL1 isdependent on inhibition of multiple class I HDACs. Supporting thisconclusion, treatment of class I HDAC-KDs with HDACi recapitulates theincreased PDL1 expression seen with WT melanoma. Finally, in in vivoexperiments combining treatment of melanoma bearing mice with anti-PDL1antibodies, mice receiving the combination treatment had a survivaladvantage over those receiving PDL1 blocking antibodies or HDACi alone(FIG. 27). These results provide a strong rationale for the evaluationof combination therapies utilizing PDL1 or PD1 blocking antibodies incombination with HDACi.

These results demonstrated that HDAC inhibitors with potency againstclass I HDACs upregulate the expression of PDL1 in melanoma cell lines.This upregulation occurs in vitro and in vivo, and is long lasting.Evaluation of IFN-γ as a mechanism of PDL1 upregualtion reveals thatPDL1 upregulation is further increased by the addition of exogneousIFN-γ. Additionally, HDACi treated melanomas fail to produce IFN-γ, TNFor TGF-b, highlighting other cytokines or an alternative mechanism ofPDL1 upregulation. Furthermore, data utilizing knock down of individualclass I HDACs does not recapitulate the PDL1 upregulation seen by HDACi.This may indicate that PDL1 upregulation is dependent on inhibition of acombination of class I HDACs. Finally, in vivo experiments showpromising results with a combination of the HDACi LBH589 and anti-PDL1blockade.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meanings as commonly understood by one of skill in the artto which the disclosed invention belongs. Publications cited herein andthe materials for which they are cited are specifically incorporated byreference.

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

1. A method for modulating Program Death Receptor Ligand 1 (PDL1) in acancer cell, comprising contacting the cell with a compositioncomprising a histone deacetylase (HDAC) inhibitor.
 2. The method claim1, wherein the HDAC inhibitor comprises a selective inhibitor of histonedeacetylase 6 (HDAC6).
 3. The method claim 2, wherein the HDAC6inhibitor is selected from the group consisting of ACY-1215, Tubacin,Tubastatin A, ST-3-06, and ST-2-92.
 4. The method of claim 1, whereinthe HDAC inhibitor comprises a pan inhibitor, a class I HDAC inhibitor,or a combination thereof. 5-12. (canceled)